Loading report..

Highlight Samples

Regex mode off

    Rename Samples

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      Regex mode off

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.


        Choose Plots

        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        Save Settings

        You can save the toolbox settings for this report to the browser.


        Load Settings

        Choose a saved report profile from the dropdown box below:

        About MultiQC

        This report was generated using MultiQC, version 1.11

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/quantms analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2022-06-16, 10:58 based on data in: /home/chengxin/pmultiqctest/test_dia/results


        pmultiqc

        pmultiqc is an module to show the pipeline performance.

        Experimental Design

        This plot shows the Proteomics Experimental Design

        This plot shows the Proteomics Experimental Design. You can see details about it in https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html

        Showing 4/4 rows and 6/6 columns.
        Spectra FileFraction_GroupFractionLabelSampleMSstats_ConditionMSstats_BioReplicate
        RD139_Narrow_UPS1_0_1fmol_inj1.mzML1111
        CT=Mixture;CN=UPS1;QY=0.1fmol
        1
        RD139_Narrow_UPS1_0_1fmol_inj2.mzML2111
        CT=Mixture;CN=UPS1;QY=0.1fmol
        1
        RD139_Narrow_UPS1_0_25fmol_inj1.mzML3112
        CT=Mixture;CN=UPS1;QY=0.25fmol
        2
        RD139_Narrow_UPS1_0_25fmol_inj2.mzML4112
        CT=Mixture;CN=UPS1;QY=0.25fmol
        2

        Summary Table

        This plot shows the quantms pipeline summary statistics

        This plot shows the quantms pipeline summary statistics

        Showing 1/1 rows and 2/2 columns.
        Total MS/MS SpectralTotal Peptide QuantifiedTotal Protein Quantified
        573300
        5729
        1605

        Pipeline Result Statistics

        This plot shows the quantms pipeline final result

        This plot shows the quantms pipeline final result. Including Sample Name、Possible Study Variables、identified the number of peptide in the pipeline、 and identified the number of modified peptide in the pipeline, eg. All data in this table are obtained from the out_msstats file. You can also remove the decoy with the remove_decoy parameter.

        Showing 4/4 rows and 7/7 columns.
        Spectra FileSample Nameconditionfractionpeptide_numunique_peptide_nummodified_peptide_numprotein_num
        RD139_Narrow_UPS1_0_1fmol_inj1.mzML
        1
        CT=Mixture;CN=UPS1;QY=0.1fmol
        1
        5407
        5407
        871
        1552
        RD139_Narrow_UPS1_0_1fmol_inj2.mzML
        1
        CT=Mixture;CN=UPS1;QY=0.1fmol
        1
        5434
        5434
        880
        1562
        RD139_Narrow_UPS1_0_25fmol_inj1.mzML
        2
        CT=Mixture;CN=UPS1;QY=0.25fmol
        1
        5572
        5572
        901
        1578
        RD139_Narrow_UPS1_0_25fmol_inj2.mzML
        2
        CT=Mixture;CN=UPS1;QY=0.25fmol
        1
        5558
        5558
        896
        1588

        Number of Peptides Per Protein

        This plot shows the number of peptides per proteins in quantms pipeline final result

        This statistic is extracted from the out_msstats file. Proteins supported by more peptide identifications can constitute more confident results.

        loading..

        Distribution of precursor charges

        This is a bar chart representing the distribution of the precursor ion charges for a given whole experiment.

        This information can be used to identify potential ionization problems including many 1+ charges from an ESI ionization source or an unexpected distribution of charges. MALDI experiments are expected to contain almost exclusively 1+ charged ions. An unexpected charge distribution may furthermore be caused by specific search engine parameter settings such as limiting the search to specific ion charges.

        loading..

        Number of Peaks per MS/MS spectrum

        This chart represents a histogram containing the number of peaks per MS/MS spectrum in a given experiment. This chart assumes centroid data. Too few peaks can identify poor fragmentation or a detector fault, as opposed to a large number of peaks representing very noisy spectra. This chart is extensively dependent on the pre-processing steps performed to the spectra (centroiding, deconvolution, peak picking approach, etc).

        loading..

        Peak Intensity Distribution

        This is a histogram representing the ion intensity vs. the frequency for all MS2 spectra in a whole given experiment. It is possible to filter the information for all, identified and unidentified spectra. This plot can give a general estimation of the noise level of the spectra.

        Generally, one should expect to have a high number of low intensity noise peaks with a low number of high intensity signal peaks. A disproportionate number of high signal peaks may indicate heavy spectrum pre-filtering or potential experimental problems. In the case of data reuse this plot can be useful in identifying the requirement for pre-processing of the spectra prior to any downstream analysis. The quality of the identifications is not linked to this data as most search engines perform internal spectrum pre-processing before matching the spectra. Thus, the spectra reported are not necessarily pre-processed since the search engine may have applied the pre-processing step internally. This pre-processing is not necessarily reported in the experimental metadata.

        loading..

        Peptides Quantification Table

        This plot shows the quantification information of peptidesin quantms pipeline final result

        The quantification information of peptides is obtained from the MSstats input file. The table shows the quantitative level and distribution of peptides in different study variables, run and peptiforms. The distribution show all the intensity values in a bar plot above and below the average intensity for all the fractions, runs and peptiforms.

        • BestSearchScore: It is equal to 1 - min(Q.Value) for DIA datasets. Then it is equal to 1 - min(best_search_engine_score[1]), which is from best_search_engine_score[1] column in mzTab peptide table for DDA datasets.
        • Average Intensity: Average intensity of each peptide sequence across all conditions with NA=0 or NA ignored.
        • Peptide intensity in each condition (Eg. CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of fractions, and then mean intensity in technical replicates/biological replicates separately. Click distribution to switch to bar plots.
        Showing 50/50 rows and 8/8 columns.
        indexProteinNamePeptideSequenceBestSearchScoreAverage IntensityCT=Mixture;CN=UPS1;QY=0.1fmolCT=Mixture;CN=UPS1;QY=0.25fmolCT=Mixture;CN=UPS1;QY=0.1fmolCT=Mixture;CN=UPS1;QY=0.25fmol
        1
        TOLA_ECOLI
        AAAEADDIFGELSSGK
        1.00000
        5.92624
        5.88893
        5.96355
        2
        G3P2_ECOLI
        AAAENIIPHTTGAAK
        0.99999
        6.12566
        6.08148
        6.16983
        3
        RLMH_ECOLI
        AAAEQSWSLSALTLPHPLVR
        0.99998
        6.23700
        6.19528
        6.27871
        4
        PDXJ_ECOLI
        AAAEVGAPFIEIHTGC(Carbamidomethyl)YADAK
        0.99966
        5.38678
        5.49758
        5.27598
        5
        RL10_ECOLI
        AAAFEGELIPASQIDR
        1.00000
        8.54788
        8.50557
        8.59019
        6
        YFGM_ECOLI
        AAAQLQQGLADTSDENLK
        1.00000
        6.68891
        6.69790
        6.67992
        7
        YFGM_ECOLI
        AAAQLQQGLADTSDENLKAVINLR
        1.00000
        6.15424
        6.03208
        6.27640
        8
        RHLE_ECOLI
        AAATGEALSLVC(Carbamidomethyl)VDEHK
        0.99998
        5.70650
        5.67986
        5.73314
        9
        SYP_ECOLI
        AAATQEMTLVDTPNAK
        1.00000
        6.27768
        6.20352
        6.35184
        10
        EUTL_ECOLI
        AAC(Carbamidomethyl)NAFTDAVLEIAR
        1.00000
        5.62924
        5.60437
        5.65410
        11
        ACRB_ECOLI
        AADGQMVPFSAFSSSR
        0.99998
        6.05977
        5.93873
        6.18081
        12
        YIDA_ECOLI
        AADGSTVAQTALSYDDYR
        0.99984
        5.69853
        5.68264
        5.71442
        13
        ADHE_ECOLI
        AADIVLQAAIAAGAPK
        1.00000
        7.67648
        7.64709
        7.70587
        14
        NARG_ECOLI
        AADLVDALGQENNPEWK
        1.00000
        5.69054
        5.64536
        5.73571
        15
        DNAK_ECOLI
        AADNKSLGQFNLDGINPAPR
        0.99984
        5.52338
        5.49575
        5.55101
        16
        OXYR_ECOLI
        AADSC(Carbamidomethyl)HVSQPTLSGQIR
        1.00000
        6.58158
        6.54958
        6.61358
        17
        TALA_ECOLI
        AAEELEKEGINC(Carbamidomethyl)NLTLLFSFAQAR
        1.00000
        6.26057
        6.20589
        6.31525
        18
        HEMY_ECOLI
        AAELAGNDTIPVEITR
        0.99995
        6.43896
        6.42564
        6.45229
        19
        SYL_ECOLI
        AAENNPELAAFIDEC(Carbamidomethyl)R
        1.00000
        6.98268
        6.94120
        7.02417
        20
        TALB_ECOLI
        AAEQLEKEGINC(Carbamidomethyl)NLTLLFSFAQAR
        1.00000
        6.97373
        6.89627
        7.05119
        21
        MBHM_ECOLI
        AAESALNIDVPVNAQYIR
        1.00000
        6.13352
        6.13039
        6.13665
        22
        DNAG_ECOLI
        AAESGVSRPVPQLKR
        0.99994
        5.09364
        4.95849
        5.22879
        23
        HDFR_ECOLI
        AAESLYLTQSAVSFR
        1.00000
        6.05307
        6.01157
        6.09457
        24
        RNE_ECOLI
        AAESRPAPFLIHQESNVIVR
        1.00000
        6.57488
        6.55722
        6.59255
        25
        HFLK_ECOLI
        AAFDDAIAARENEQQYIR
        1.00000
        5.77820
        5.63543
        5.92097
        26
        AROF_ECOLI
        AAFPLSLQQEAQIADSR
        1.00000
        5.92732
        5.93057
        5.92407
        27
        AROF_ECOLI
        AAFPLSLQQEAQIADSRK
        0.99984
        5.76026
        5.73177
        5.78874
        28
        BOLA_ECOLI
        AAFQPVFLEVVDESYR
        1.00000
        6.72860
        6.71178
        6.74543
        29
        CLPB_ECOLI
        AAGATTANITQAIEQMR
        1.00000
        6.06974
        5.97263
        6.16686
        30
        YBIS_ECOLI
        AAGEPLPAVVPAGPDNPMGLYALYIGR
        1.00000
        5.94884
        5.83808
        6.05959
        31
        SDHA_ECOLI
        AAGLHLQESIAEQGALR
        1.00000
        5.42244
        5.42948
        5.41540
        32
        TALA_ECOLI
        AAGLSQYEHLIDDAIAWGK
        0.99984
        5.17878
        5.11623
        5.24132
        33
        TALA_ECOLI
        AAGLSQYEHLIDDAIAWGKK
        1.00000
        5.82005
        5.77630
        5.86380
        34
        ADHE_ECOLI
        AAGVETEVFFEVEADPTLSIVR
        0.99999
        6.46527
        6.51683
        6.41371
        35
        ADHE_ECOLI
        AAGVETEVFFEVEADPTLSIVRK
        0.99984
        6.82885
        6.77579
        6.88191
        36
        ENO_ECOLI
        AAGYELGKDITLAMDC(Carbamidomethyl)AASEFYK
        1.00000
        6.64634
        6.62909
        6.66359
        37
        YEBE_ECOLI
        AAHQDEPQFGAQSTPLDER
        0.99984
        5.64827
        5.62198
        5.67456
        38
        RIBB_ECOLI
        AAIADGAKPSDLNRPGHVFPLR
        1.00000
        6.46193
        6.43130
        6.49256
        39
        DEOC_ECOLI
        AAIAYGADEVDVVFPYR
        1.00000
        7.04750
        6.99277
        7.10224
        40
        IDH_ECOLI
        AAIEYAIANDRDSVTLVHK
        1.00000
        6.28684
        6.26890
        6.30479
        41
        DPO1_ECOLI
        AAINAPMQGTAADIIKR
        0.99984
        5.87444
        5.85167
        5.89720
        42
        SYFA_ECOLI
        AAISQASDVAALDNVR
        1.00000
        6.88310
        6.87875
        6.88744
        43
        SYFA_ECOLI
        AAISQASDVAALDNVRVEYLGK
        1.00000
        6.04132
        5.98363
        6.09900
        44
        MUKF_ECOLI
        AAISSC(Carbamidomethyl)ELLLSETSGTLR
        0.99984
        5.45034
        5.39500
        5.50568
        45
        MSCM_ECOLI
        AAKPAQPEVVEALQSALNALEER
        0.99993
        5.25606
        5.16930
        5.34283
        46
        AMPN_ECOLI
        AALEQLKGLENLSGDLYEK
        1.00000
        6.25426
        6.19468
        6.31384
        47
        DBHA_ECOLI
        AALESTLAAITESLK
        1.00000
        7.30296
        7.31293
        7.29298
        48
        HEM3_ECOLI
        AALPPEISLPAVGQGAVGIEC(Carbamidomethyl)R
        0.99989
        6.30968
        6.27974
        6.33962
        49
        SDHA_ECOLI
        AALQISQSGQTC(Carbamidomethyl)ALLSK
        0.99991
        5.55626
        5.47807
        5.63444
        50
        DHE4_ECOLI
        AANAGGVATSGLEMAQNAAR
        1.00000
        5.72703
        5.66062
        5.79344
        First Page Previous PageNext Page Last PagePage/Total Pages

        Protein Quantification Table

        This plot shows the quantification information of proteinsin quantms pipeline final result

        The quantification information of proteins is obtained from the msstats input file. The table shows the quantitative level and distribution of proteins in different study variables and run.

        • Peptides_Number: The number of peptides for each protein.
        • Average Intensity: Average intensity of each protein across all conditions with NA=0 or NA ignored.
        • Protein intensity in each condition (Eg. CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of peptides.Click distribution to switch to bar plots.
        Showing 50/50 rows and 6/6 columns.
        ProteinNamePeptides_NumberAverage IntensityCT=Mixture;CN=UPS1;QY=0.1fmolCT=Mixture;CN=UPS1;QY=0.25fmolCT=Mixture;CN=UPS1;QY=0.1fmolCT=Mixture;CN=UPS1;QY=0.25fmol
        3PASE_ECOLI
        1
        5.62306
        5.60463
        5.64150
        5DNU_ECOLI
        1
        5.18693
        5.11178
        5.26208
        6PGD_ECOLI
        10
        7.42942
        7.41428
        7.44456
        6PGL_ECOLI
        2
        6.50260
        6.47213
        6.53307
        AAEB_ECOLI
        1
        6.17840
        6.14101
        6.21578
        AAS_ECOLI
        4
        6.06861
        6.07277
        6.06445
        AAT_ECOLI
        2
        7.17292
        7.15145
        7.19440
        ABGT_ECOLI
        1
        5.23376
        5.33010
        5.13743
        ACCA_ECOLI
        11
        7.75792
        7.71705
        7.79878
        ACCC_ECOLI
        12
        7.61524
        7.57807
        7.65242
        ACCD_ECOLI
        4
        6.95665
        6.94380
        6.96950
        ACEA_ECOLI
        10
        7.20604
        7.16455
        7.24753
        ACFD_ECOLI
        8
        6.82809
        6.79050
        6.86569
        ACKA_ECOLI
        10
        8.29284
        8.26443
        8.32125
        ACNA_ECOLI
        5
        6.10554
        6.03155
        6.17954
        ACNB_ECOLI
        11
        7.55688
        7.52042
        7.59335
        ACRA_ECOLI
        6
        7.49514
        7.45093
        7.53935
        ACRB_ECOLI
        6
        6.86423
        6.80422
        6.92424
        ACSA_ECOLI
        2
        5.59331
        5.63552
        5.55110
        ACUI_ECOLI
        5
        7.03398
        6.95830
        7.10966
        ACYP_ECOLI
        1
        5.61388
        5.60391
        5.62384
        ADD_ECOLI
        5
        7.28189
        7.25590
        7.30788
        ADEC_ECOLI
        1
        5.38668
        5.35270
        5.42067
        ADHE_ECOLI
        36
        8.65016
        8.61049
        8.68982
        ADHP_ECOLI
        2
        6.07902
        6.07556
        6.08247
        ADIA_ECOLI
        3
        5.91748
        5.85021
        5.98476
        ADPP_ECOLI
        2
        6.61200
        6.58045
        6.64355
        AGP_ECOLI
        3
        6.13662
        6.10643
        6.16680
        AHPC_ECOLI
        9
        8.12726
        8.09729
        8.15722
        AHPF_ECOLI
        9
        7.59356
        7.57594
        7.61117
        AHR_ECOLI
        1
        5.05767
        5.13523
        4.98011
        AK1H_ECOLI
        7
        6.48752
        6.45929
        6.51575
        AK2H_ECOLI
        4
        6.50094
        6.47209
        6.52980
        AK3_ECOLI
        5
        6.58938
        6.53665
        6.64211
        ALAA_ECOLI
        3
        6.60599
        6.58144
        6.63054
        ALAC_ECOLI
        5
        6.56726
        6.51161
        6.62291
        ALDB_ECOLI
        1
        6.04168
        6.01046
        6.07289
        ALF1_ECOLI
        2
        5.44720
        5.08834
        5.80606
        ALF_ECOLI
        10
        8.13548
        8.11628
        8.15468
        ALKH_ECOLI
        3
        6.64010
        6.56865
        6.71154
        ALR1_ECOLI
        3
        6.66391
        6.63045
        6.69737
        AMIA_ECOLI
        1
        5.80634
        5.76583
        5.84686
        AMIB_ECOLI
        2
        5.72767
        5.69326
        5.76208
        AMIC_ECOLI
        5
        5.98195
        5.89629
        6.06762
        AMID_ECOLI
        1
        4.52776
        4.35834
        4.69717
        AMN_ECOLI
        8
        6.76504
        6.74232
        6.78775
        AMPA_ECOLI
        7
        7.26489
        7.23293
        7.29686
        AMPC_ECOLI
        2
        6.11671
        6.06209
        6.17133
        AMPH_ECOLI
        2
        6.15217
        6.09222
        6.21212
        AMPN_ECOLI
        7
        7.10628
        7.08197
        7.13058
        First Page Previous PageNext Page Last PagePage/Total Pages

        nf-core/quantms Software Versions

        are collected at run time from the software output.

        Process Name Software Version
        ASSEMBLE_EMPIRICAL_LIBRARY DIA-NN 1.8.1
        CUSTOM_DUMPSOFTWAREVERSIONS python 3.9.5
        yaml 5.4.1
        DIANNCFG sdrf-pipelines 0.0.21
        DIANNCONVERT sdrf-pipelines 0.0.21
        DIANNSUMMARY DIA-NN 1.8.1
        DIANN_PRELIMINARY_ANALYSIS DIA-NN 1.8.1
        INDIVIDUAL_FINAL_ANALYSIS DIA-NN 1.8.1
        MSSTATS bioconductor-msstats 4.2.0
        r-base 4.1.2
        SAMPLESHEET_CHECK sdrf-pipelines 0.0.21
        SDRFPARSING sdrf-pipelines 0.0.21
        THERMORAWFILEPARSER ThermoRawFileParser 1.3.4
        Workflow Nextflow 21.10.6
        nf-core/quantms 1.1dev

        nf-core/quantms Workflow Summary

        - this information is collected when the pipeline is started.

        Core Nextflow options

        runName
        voluminous_thompson
        containerEngine
        docker
        launchDir
        /home/chengxin/newPR/quantms
        workDir
        /home/chengxin/newPR/quantms/work
        projectDir
        /home/chengxin/newPR/quantms
        userName
        chengxin
        profile
        test_dia,docker
        configFiles
        /home/chengxin/newPR/quantms/nextflow.config

        Input/output options

        input
        /home/chengxin/diatestdata/PXD026600/PXD026600Partial2.sdrf.tsv
        outdir
        ./results_dia

        Protein database

        database
        /home/chengxin/diatestdata/PXD026600/REF_EColi_K12_UPS1_combined.fasta

        Database search

        allowed_missed_cleavages
        1
        instrument
        N/A
        max_precursor_charge
        3
        min_peptide_length
        15
        max_peptide_length
        30
        max_mods
        2

        Modification localization

        luciphor_debug
        N/A

        PSM re-scoring (general)

        run_fdr_cutoff
        0.10

        PSM re-scoring (Percolator)

        description_correct_features
        N/A

        Consensus ID

        consensusid_considered_top_hits
        N/A
        min_consensus_support
        N/A

        Isobaric analyzer

        select_activation
        HCD

        Protein Quantification (DDA)

        ratios
        N/A
        normalize
        N/A
        fix_peptides
        N/A

        DIA-NN

        acquisition_method
        N/A
        mass_acc_ms2
        13
        mass_acc_ms1
        7
        scan_window
        8
        min_pr_mz
        350
        max_pr_mz
        950
        min_fr_mz
        500
        max_fr_mz
        1500
        diann_normalize
        N/A

        Statistical post-processing

        contrasts
        pairwise

        Quality control

        enable_pmultiqc
        true

        Institutional config options

        config_profile_name
        Test profile for DIA
        config_profile_description
        Minimal test dataset to check pipeline function for the data-independent acquisition pipeline branch.

        Max job request options

        max_cpus
        2
        max_memory
        6 GB
        max_time
        2d

        Generic options

        hostnames
        N/A